Yutaro Hirono

Thank you for the very straightforward suggestion! I will try using --minimize, or --minimize --local_only. Does that sound appropriate? Additionally, is smina capable of performing such alignment? For now, I am going to use other software like RDKit.

Thank you for the very straightforward suggestion! I will try using --minimize, or --minimize --local_only. Does that sound appropriate?

Thank you for the very straightforward suggestion! I will try --minimize, --local_only.

Thank you very much for your quick reply! I will define new atom types and prepare the PDBQT files accordingly. Actually, the problem I am working on is the lack of docking poses where the common substructure of my ligands (the scaffold) is placed in the "correct" location. Is it possible to apply constraints on the positions of specific atoms in my ligands?

Dear Dr. Koes, We would like to reduce the van der Waals radius of atoms in a fragmental moiety that are commonly found in our ligand molecules. Can I set up such calculations by using an option implemeted in smina ? Thank you in advance, Best regards, Yutaro.